I've been examining the eBayes function in Limma using some affymetrix data we have. The default proportion setting: 0.01 I think is probably wrong for the comparison of tissue groups I have. Is there a rational way to estimate/guesstimate the correct proportion? Or isn't that the point anyway? Stephen ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

Dear Stephen, A good question. It is actually very easy mathematically to estimate the proportion ('p') from the eBayes model. We don't do this at the moment because we don't think the simply heirarchical model fits the data well enough for the estimate of this parameter to be biologically meaningful. We thought it better to use a plug-in value rather than to risk misleading people re the true proportion of differentially expressed genes in their samples. If you like, you can simply set 'p' to a value you're more comfortable with. In any case, this will not change the ranking of the genes using the log-odds. And the moderated t-statistics provide an almost equivalent inferential method that does not require 'p' at all. Getting a good biologically believable estimate of 'p' is a non- trivial problem which we and others are working on. If you want a data driven method right now try this: convert the log-odds of differential expression to probabilities, then vary 'p' until it matches the mean probability. Regards Gordon At 12:49 AM 9/12/2003, Stephen Henderson wrote: > I've been examining the eBayes function in Limma using some affymetrix data >we have. The default proportion setting: 0.01 I think is probably wrong for >the comparison of tissue groups I have. > >Is there a rational way to estimate/guesstimate the correct proportion? Or >isn't that the point anyway? > >Stephen